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ORIGINAL RESEARCH article

Front. Microbiol.

Sec. Antimicrobials, Resistance and Chemotherapy

Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1662113

This article is part of the Research TopicAntimicrobial Resistance: Tracking and Tackling in the Food ChainView all 7 articles

Antimicrobial resistance reservoirs in salmon and broiler processing environments, sidestreams, and waste discharges

Provisionally accepted
Thorben ReicheThorben Reiche1*Anita Nordeng JakobsenAnita Nordeng Jakobsen1Mihai MaresMihai Mares2Sunniva HoelSunniva Hoel1Anne TøndervikAnne Tøndervik3Tonje Marita Bjerkan HeggesetTonje Marita Bjerkan Heggeset3Tone HaugenTone Haugen3Andreas Husby TømmerdalAndreas Husby Tømmerdal3Gunn BroliGunn Broli3Husnain Amir ButtHusnain Amir Butt1Iris Olene BårdsenIris Olene Bårdsen1Gunhild HageskalGunhild Hageskal3
  • 1Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
  • 2Department of Public Health, "Ion Ionescu de la Brad" University of Life Sciences, Iași, Romania
  • 3Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway

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Mapping reservoirs of antimicrobial resistance (AMR) across food value chains and their environmental dissemination pathways is essential for limiting the spread and impact of AMR. The aim of this study was to investigate the prevalence of AMR genes and bacteria in sidestream materials, waste discharges, and processing environments of salmon and broiler. A targeted hybrid capture-based sequencing approach was used to characterize the resistome in samples collected from four processing plants, revealing a diverse range of AMR genes. Among these, we found several high-risk AMR genes, including the multidrug resistance genes TolC and mdtE, tetracycline genes tet(L) and tet(M), aminoglycoside genes APH(3')-IIIa and APH(6)-Id, and beta-lactam genes mecA and mecR1. Overall, the highest numbers of AMR genes were found in samples of process wastewater and sludge, ranging from 32 to 330 unique genes. More than 300 bacterial isolates, including Enterobacterales, Enterococcus and Pseudomonas spp. were also collected and identified, and a subset was tested for antibiotic susceptibility. Antibiotic resistance among Enterococcus and Pseudomonas spp. was low. Quinolone-resistant Escherichia coli (QREC) were detected in waste discharges from two broiler processing plants, while multidrug resistant (MDR) E. coli were found only in one plant. Whole genome sequencing of MDR isolates revealed multiple plasmids and AMR genes such as sul2, ant(3'')-Ia, qnrS1, and blaCTX-M-1. Our study highlights that wastewater from food industries can contribute to the release of AMR bacteria and genes to the environment. While the prevalence of AMR bacteria in sidestream materials was low among the isolates in our collection, numerous AMR genes were detected, which may be re-introduced to new production systems.slettet: Antimicrobial resistance genes and bacteria in sidestream materials, waste discharges and processing environments of salmon and broiler

Keywords: chicken, Poultry, Aquaculture, Rest raw material, wastewater, ARG, MDR, QIAseq xHYB. (Min.5-Max. 8)

Received: 08 Jul 2025; Accepted: 14 Aug 2025.

Copyright: © 2025 Reiche, Jakobsen, Mares, Hoel, Tøndervik, Heggeset, Haugen, Tømmerdal, Broli, Butt, Bårdsen and Hageskal. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Thorben Reiche, Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway

Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.

Supplementary Material